Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structures of rotary ATP synthase from during proton powered ATP synthesis.
Journal, issue, pages	Sci Adv, Vol. 11, Issue 42, Page eadx8771, Year 2025
Publish date	Oct 17, 2025
Authors	Atsuki Nakano / Jun-Ichi Kishikawa / Nishida Yui / Kyosuke Sugawara / Yuto Kan / Christoph Gerle / Hideki Shigematsu / Kaoru Mitsuoka / Ken Yokoyama /
PubMed Abstract	ATP synthases are rotary molecular machines that use the proton motive force to rotate the central rotor complex relative to the surrounding stator apparatus, thereby coupling the ATP synthesis. We ...ATP synthases are rotary molecular machines that use the proton motive force to rotate the central rotor complex relative to the surrounding stator apparatus, thereby coupling the ATP synthesis. We reconstituted the V/A-ATPase into liposomes and performed structural analysis using cryo-EM under conditions where the proton motive force was applied in the presence of ADP and Pi. ATP molecules were bound at two of the three catalytic sites of V/A-ATPase, confirming that the structure represents a state adopted during ATP synthesis. In this structure, the catalytic site closes upon binding of ADP and Pi through an induced fit mechanism. Multiple structures were obtained where the membrane-embedded rotor ring was in a different position relative to the stator. By comparing these structures, we found that torsion occurs in both the central rotor and the peripheral stator during 31° rotation of rotor ring. These structural snapshots of V/A-ATPase provide crucial insights into the mechanism of rotary catalysis of ATP synthesis.
External links	Sci Adv / PubMed:41105777 / PubMed Central
Methods	EM (single particle)
Resolution	2.2 - 4.67 Å
Structure data	63904 9u6f EMDB-63904, PDB-9u6f: Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes, state1 Method: EM (single particle) / Resolution: 2.2 Å 63905 9u6g EMDB-63905, PDB-9u6g: Cryo-EM structure of the Vo domain of V/A-ATPase in liposomes, state1 Method: EM (single particle) / Resolution: 2.7 Å EMDB-63906: Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes, state2 Method: EM (single particle) / Resolution: 2.5 Å EMDB-63907: Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes, state3 Method: EM (single particle) / Resolution: 2.6 Å 63908 9u6h EMDB-63908, PDB-9u6h: Cryo-EM structure of the Vo domain of V/A-ATPase in liposomes, state2 Method: EM (single particle) / Resolution: 3.0 Å 63909 9u6i EMDB-63909, PDB-9u6i: Cryo-EM structure of the Vo domain of V/A-ATPase in liposomes, state3 Method: EM (single particle) / Resolution: 3.0 Å 63910 9u6j EMDB-63910, PDB-9u6j: Cryo-EM structure of the Vo domain of V/A-ATPase under pmf condition, State3A Method: EM (single particle) / Resolution: 4.02 Å 63911 9u6k EMDB-63911, PDB-9u6k: Cryo-EM structure of the Vo domain of V/A-ATPase under pmf condition, State3B Method: EM (single particle) / Resolution: 4.1 Å 63912 9u6l EMDB-63912, PDB-9u6l: Cryo-EM structure of the Vo domain of V/A-ATPase under pmf condition, State3C Method: EM (single particle) / Resolution: 4.67 Å 63913 9u6m EMDB-63913, PDB-9u6m: Cryo-EM structure of the Vo domain of V/A-ATPase under pmf condition, state3D Method: EM (single particle) / Resolution: 4.64 Å 63914 9u6n EMDB-63914, PDB-9u6n: Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes under no pmf condition, state1W Method: EM (single particle) / Resolution: 2.85 Å 63915 9u6o EMDB-63915, PDB-9u6o: Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes under no pmf condition, state1M Method: EM (single particle) / Resolution: 2.8 Å 63916 9u6p EMDB-63916, PDB-9u6p: Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes under no pmf condition, state1N Method: EM (single particle) / Resolution: 2.85 Å EMDB-63917: Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes under no pmf condition, state2 Method: EM (single particle) / Resolution: 3.0 Å EMDB-63918: Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes under no pmf condition, state3 Method: EM (single particle) / Resolution: 3.0 Å 63919 9u6q EMDB-63919, PDB-9u6q: Cryo-EM structure of the Vo domain of V/A-ATPase in liposomes under no pmf condition,state1 Method: EM (single particle) / Resolution: 3.6 Å 63922 9u6t EMDB-63922, PDB-9u6t: Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes under pmf condition, state1W Method: EM (single particle) / Resolution: 2.9 Å 63923 9u6u EMDB-63923, PDB-9u6u: Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes under pmf condition, state1M Method: EM (single particle) / Resolution: 2.9 Å 63924 9u6v EMDB-63924, PDB-9u6v: Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes under pmf condition, state1N Method: EM (single particle) / Resolution: 3.0 Å 63925 9u6w EMDB-63925, PDB-9u6w: Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes under pmf condition, state3W Method: EM (single particle) / Resolution: 3.1 Å 63926 9u6x EMDB-63926, PDB-9u6x: Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes under pmf condition, state3M Method: EM (single particle) / Resolution: 3.0 Å 63927 9u6y EMDB-63927, PDB-9u6y: Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes under pmf condition, state3N Method: EM (single particle) / Resolution: 2.9 Å EMDB-63928: Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes under pmf condition,state2 Method: EM (single particle) / Resolution: 2.8 Å EMDB-63929: Cryo-EM structure of the Vo domain of V/A-ATPase in liposomes under pmf condition,state1 Method: EM (single particle) / Resolution: 3.2 Å EMDB-63930: Cryo-EM structure of the Vo domain of V/A-ATPase in liposomes under pmf condition,state2 Method: EM (single particle) / Resolution: 3.6 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM ChemComp-HOH: WATER ChemComp-PO4: PHOSPHATE ION
Source	thermus thermophilus hb8 (bacteria)
Keywords	MOTOR PROTEIN / ATP synthase / V ATPase / V1 ATPase